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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        Tool Citations

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        About MultiQC

        This report was generated using MultiQC, version 1.31

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-10-24, 20:57 CDT based on data in:
        • /project/lbarreiro/USERS/austin/slamseq/data/fastp_reports
        • /project/lbarreiro/USERS/austin/slamseq/logs/hisat-3n/qc

        General Statistics

        Showing 4/4 rows and 6/10 columns.
        Sample Name% Aligned% Duplication% > Q30Mb Q30 basesReads After FilteringGC content% PF% AdapterMean R1 LengthMean R2 Length
        LB-HT-28s-HT-10_S10
        47.7%
        94.1%
        64392.3Mb
        436.1M
        49.7%
        97.7%
        4.6%
        158.0bp
        158.0bp
        LB-HT-28s-HT-16_S16
        37.5%
        93.7%
        59116.6Mb
        404.1M
        51.2%
        97.4%
        7.7%
        158.0bp
        158.0bp
        LB-HT-28s-HT-17_S17
        50.0%
        0.0%
        68.2%
        0.0Mb
        0.0M
        57.7%
        14.7%
        0.0%
        158.0bp
        158.0bp
        LB-HT-28s-HT-18_S18
        82.3%
        39.3%
        93.8%
        56778.4Mb
        386.7M
        50.0%
        97.5%
        6.2%
        158.0bp
        158.0bp

        HISAT2

        Maps DNA or RNA reads against a genome or a population of genomes.URL: https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4

        Please note that single mate alignment counts are halved to tally with pair counts properly.

        Created with MultiQC

        fastp

        Version: 1.0.1

        All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560

        Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

        Filtered Reads

        Filtering statistics of sampled reads.

        Created with MultiQC

        Insert Sizes

        Insert size estimation of sampled reads.

        Created with MultiQC

        Sequence Quality

        Average sequencing quality over each base of all reads.

        Created with MultiQC

        GC Content

        Average GC content over each base of all reads.

        Created with MultiQC

        N content

        Average N content over each base of all reads.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        fastp1.0.1

        MultiQC v1.31 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.